Fresh and fresh-cut tomatoes are high in phytonutrients. But the illness outbreaks associated with contaminated tomatoes have significantly impacted public health and the industry’s economic well-being. Scientific information is critically needed to develop an effective, practical food safety standard to reduce pathogen contamination. The aim of this study was to assess factors impacting the deterioration of tomato wash water quality and indigenous microorganisms during a simulated dump tank washing process. Freshly harvested grape tomatoes were sorted into four groups: prime, defective, under-ripened, and non-tomato debris. Tomatoes with leaf-stem harvest debris, combined or separately, were washed in tap water with or without free chlorine (FC). Water samples were analyzed for total dissolved solids, turbidity, chemical oxygen demand, and chlorine demand. Microbial populations in water and on tomatoes as impacted by chlorine concentration and water filtration (300 µm) were also determined. Results showed that field debris and defective tomatoes were the major contributors to microbial counts in wash water. Field debris, although only accounting for <1% of the total weight of harvested material, contributed 37.84% of total dissolved solids, 46.15% of turbidity, 48.77% of chemical oxygen demand, and 50.55% of chlorine demand in the wash water. Water quality deterioration was proportional to the cumulative quantity of tomatoes and debris washed, and FC at 5 mg/L or higher significantly reduced the Enterobacteriaceae, aerobic mesophilic bacteria, and yeast and mold populations. This study underscores the importance to minimize the presence of field debris and defective fruits from harvested grape tomatoes in order to reduce the microbial load and wash water quality deterioration of water quality in post-harvest tomato washing. This information is beneficial to the development of data-driven harvesting and packinghouse food safety practices for grape tomatoes.